From: Ben Soares Date: Tue, 2 Jul 2019 19:16:01 +0000 (+0100) Subject: JAL-3337 Tidied up j8libs in THIRDPARTYLIBS. Replaced jersey-*-1.19.jar with jersey... X-Git-Tag: Release_2_11_0~2^2~2^2~1 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9c93d8688181b15cae619659144e3f1310d22933;p=jalview.git JAL-3337 Tidied up j8libs in THIRDPARTYLIBS. Replaced jersey-*-1.19.jar with jersey-*-1.19.4.jar in j8lib. Removed lib/ folder from sourceDist. Added instructions for running testNG with a specific group of tests to building.md --- diff --git a/THIRDPARTYLIBS b/THIRDPARTYLIBS index 296ae17..348827e 100644 --- a/THIRDPARTYLIBS +++ b/THIRDPARTYLIBS @@ -15,53 +15,78 @@ Licensing information for each library is given below: j8lib: -JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ -Jmol-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ -VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty. http://varna.lri.fr activation.jar apache-mime4j-0.6.jar axis.jar -castor-1.1-cycle-xml.jar +biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE +biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE commons-codec-1.3.jar -commons-discovery.jar +commons-compress-1.18.jar commons-logging-1.1.1.jar -commons-logging.jar -commons-net-3.3.jar -groovy-all-2.4.6-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip +getdown-core.jar Getdown license - https://github.com/threerings/getdown/blob/master/LICENSE +groovy-all-2.4.12-indy.jar APL 2.0 License - downloaded and extracted from https://dl.bintray.com/groovy/maven/apache-groovy-binary-2.4.6.zip +htsjdk-2.12.0.jar built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute httpclient-4.0.3.jar httpcore-4.0.1.jar httpmime-4.0.3.jar +intervalstore-v1.0.jar +jabaws-min-client-2.2.0.jar +java-json.jar jaxrpc.jar +jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jetty-http-9.2.10.v20150310.jar +jetty-io-9.2.10.v20150310.jar +jetty-server-9.2.10.v20150310.jar +jetty-util-9.2.10.v20150310.jar +jfreesvg-2.1.jar GPL v3 licensed library from the JFree suite - http://www.jfree.org/jfreesvg/ +JGoogleAnalytics_0.3.jar APL 2.0 License - http://code.google.com/p/jgoogleanalytics/ jhall.jar -jswingreader-0.3.jar : Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12 +Jmol-14.6.4_2016.10.26.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ +json_simple-1.1.jar Apache 2.0 license - downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised) +jsoup-1.8.1.jar +jsr311-api-1.1.1.jar +jswingreader-0.3.jar Apache license - built from http://jswingreader.sourceforge.net/ svn/trunk v12 +libquaqua64-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ +libquaqua-8.0.jnilib.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ log4j-1.2.8.jar mail.jar -miglayout-4.0-swing.jar BSD http://www.migcalendar.com/miglayout/versions/4.0/license.txt -min-jaba-client.jar +miglayout-4.0-swing.jar BSD - http://www.migcalendar.com/miglayout/versions/4.0/license.txt +quaqua-filechooser-only-8.0.jar quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ regex.jar saaj.jar +servlet-api-3.1.jar +slf4j-api-1.7.7.jar +slf4j-log4j12-1.7.7.jar vamsas-client.jar +VAqua5-patch.jar This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses. +VARNAv3-93.jar GPL licenced software by K�vin Darty, Alain Denise and Yann Ponty - http://varna.lri.fr wsdl4j.jar xercesImpl.jar xml-apis.jar -json_simple-1.1.jar : Apache 2.0 license : downloaded from https://code.google.com/p/json-simple/downloads/list (will move to 1.1.1 version when jalview is mavenised and osgi-ised) -jfreesvg-2.1.jar : GPL v3 licensed library from the JFree suite: http://www.jfree.org/jfreesvg/ - -quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/ - -vaqua5-patch: This is a patched version of VAqua v5 (latest stable) by Alan Snyder et al. GPLv3 with Classpath exception, also includes contributions from Quaqua: http://violetlib.org/vaqua/overview.html - see doc/patching-vaqua.txt for patch details, and http://issues.jalview.org/browse/JAL-2988 for details of the bug that the patch addresses. - -lib/htsjdk-2.12.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute - -lib/biojava-core-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE - -lib/biojava-ontology-4.1.0.jar LGPLv2.1 - latest license at https://github.com/biojava/biojava/blob/master/LICENSE Libraries for Test Suite -utils/classgraph-4.1.6.jar: BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview - version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6 +utils/axis-ant.jar +utils/ant-contrib-1.0b3.jar +utils/hamcrest-core-1.3.jar +utils/roxes-ant-tasks-1.2-2004-01-30.jar +utils/proguard_5.3.3.jar +utils/jhindexer.jar +utils/junit-4.12.jar +utils/jhall.jar +utils/classgraph-4.1.6.jar BSD License - allows recovery of classpath for programmatic construction of a Java command line to launch Jalview version 4.1.6 downloaded from https://mvnrepository.com/artifact/io.github.classgraph/classgraph/4.1.6 +utils/testnglibs/guava-base-r03.jar +utils/testnglibs/guava-collections-r03.jar +utils/testnglibs/bsh-2.0b4.jar +utils/testnglibs/snakeyaml.jar +utils/testnglibs/testng-sources.jar +utils/testnglibs/testng.jar +utils/testnglibs/junit-4.12.jar +utils/testnglibs/jcommander.jar +utils/wsdl4j.jar Additional dependencies @@ -86,10 +111,8 @@ javax.xml.rpc-api-1.1.2.jar CDDL + GPLv2 with classpath exception - https://oss. javax.xml.soap-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/javax.xml.soap/blob/master/LICENSE jaxb-api-2.3.1.jar CDDL 1.1 + GPL2 w/ CPE - https://oss.oracle.com/licenses/CDDL+GPL-1.1 jaxb-runtime-2.3.2.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php -jaxws-api.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md -jersey-client-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html -jersey-core-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html -jersey-json-1.19.4.jar CDDL 1.1 + GPL2 w/ CPE - http://glassfish.java.net/public/CDDL+GPL_1_1.html +jaxws-api-2.3.1.jar CDDL + GPLv2 with classpath exception - https://github.com/javaee/jax-ws-spec/blob/master/LICENSE.md +Jmol-14.6.4_2016.10.26-no_netscape.jar GPL/LGPLv2 http://sourceforge.net/projects/jmol/files/ jsr311-api-1.1.1.jar CDDL License - http://www.opensource.org/licenses/cddl1.php mimepull-1.9.11.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php policy-2.7.6.jar Eclipse Distribution License - v 1.0 - http://www.eclipse.org/org/documents/edl-v10.php diff --git a/build.gradle b/build.gradle index 76284e9..2332643 100644 --- a/build.gradle +++ b/build.gradle @@ -1205,6 +1205,7 @@ task sourceDist (type: Tar) { exclude ("**/*locales") exclude ("*locales/**") exclude ("utils/InstallAnywhere") + exclude (libDir) exclude (getdown_files_dir) exclude (getdown_website_dir) diff --git a/doc/building.md b/doc/building.md index 9648b9c..cc3d7f2 100644 --- a/doc/building.md +++ b/doc/building.md @@ -327,6 +327,14 @@ gradle test These normally take around 5 - 10 minutes to complete and outputs its full results into the `tests/` folder. A summary of results should appear in your console. +You can run different defined groups of tests with + +```bash +gradle test -PtestngGroups=Network +``` + +Available groups are Functional (default), Network, External. + ### Installer packaging with *install4j* @@ -490,4 +498,4 @@ in the `jalview` root folder. --- -[Jalview Development Team](mailto:help@jalview.org) \ No newline at end of file +[Jalview Development Team](mailto:help@jalview.org) diff --git a/j8lib/jersey-client-1.19.jar b/j8lib/jersey-client-1.19.4.jar similarity index 82% rename from j8lib/jersey-client-1.19.jar rename to j8lib/jersey-client-1.19.4.jar index c9e0f56..0588ee2 100644 Binary files a/j8lib/jersey-client-1.19.jar and b/j8lib/jersey-client-1.19.4.jar differ diff --git a/j8lib/jersey-core-1.19.jar b/j8lib/jersey-core-1.19.4.jar similarity index 85% rename from j8lib/jersey-core-1.19.jar rename to j8lib/jersey-core-1.19.4.jar index 92feb63..e800c60 100644 Binary files a/j8lib/jersey-core-1.19.jar and b/j8lib/jersey-core-1.19.4.jar differ diff --git a/j8lib/jersey-json-1.19.jar b/j8lib/jersey-json-1.19.4.jar similarity index 85% rename from j8lib/jersey-json-1.19.jar rename to j8lib/jersey-json-1.19.4.jar index b609411..c79271b 100644 Binary files a/j8lib/jersey-json-1.19.jar and b/j8lib/jersey-json-1.19.4.jar differ